Fig. 5

CSS integrates scRNA-seq data generated using different technologies. a Joint analysis of cerebral organoid scRNA-seq data generated using different technologies without integration. Cell type annotation is performed in each data set separately (top). Joint UMAP embedding is generated without integration and colored by cell types (bottom left) and technologies (bottom right), respectively. b UMAP embeddings based on different integration methods, colored by cell type annotation (top) and technology (bottom). c Heatmaps showing summarized performance metrics. Numbers show the ranking of different integration methods based on each metric. d Joint analysis of public PBMC scRNA-seq data generated using different methods without integration. UMAP embeddings are colored by annotated cell types (top) and methods (bottom). e UMAP embeddings based on different integration methods, colored by cell type annotation (top) and methods (bottom). f Heatmaps showing summarized performance metrics. Numbers show the ranking of different integration methods based on different metrics